The eponymous Algernon is a laboratory mouse who has undergone surgery to increase his intelligence by artificial means. The story is told by a series of progress reports written by Charlie Gordon, the first human test subject for the surgery, and it touches upon many different ethical and moral themes such as the treatment of the mentally disabled.[4][5]

Although the book has often been challenged for removal from libraries in the US and Canada,[6] sometimes successfully,[7] it is regularly taught in schools around the world[8] and has been adapted many times for television, theatre, radio, and as the Academy Award–winning film Charly.

The ideas for Flowers for Algernon developed over a period of 14 years and were inspired by numerous events in Keyes' life, starting in 1945 with Keyes's personal conflict with his parents who were pushing him through a pre-medical education in spite of his desire to pursue a writing career. Keyes felt that his education was driving a wedge between him and his parents and this led him to wonder what would happen if it were possible to increase a person’s intelligence.[8][9][10][5] A pivotal moment occurred in 1957 while Keyes was teaching English to students with special needs; one of them asked him if it would be possible to be put into a regular class if he worked hard and became smart.[10][11][5] Keyes also witnessed the dramatic progress of another learning-disabled student who regressed after he was removed from regular lessons. Keyes said that "When he came back to school, he had lost it all. He could not read. He reverted to what he had been. It was a heart-breaker."[5]

Different characters in the book were also based on people in Keyes's life. The character of Algernon was inspired by a university dissection class, and the name was inspired by the poet Algernon Charles Swinburne.[10] Nemur and Strauss, the scientists who develop the intelligence-enhancing surgery in the story, were based on professors Keyes met while studying psychoanalysis in graduate school.[10]

In 1958, Keyes was approached by Galaxy Science Fiction magazine to write a story, at which point the different elements of Flowers for Algernon fell into place.[10] When the story was submitted to Galaxy, however, editor Horace Gold suggested changing the ending so that Charlie retained his intelligence, married Alice Kinnian, and lived happily ever after.[10][12] Keyes refused to make the change and sold the story to The Magazine of Fantasy and Science Fiction instead.[10]

Keyes worked on the expanded novel between 1962 and 1965[13] and first tried to sell it to Doubleday, but they also wanted to change the ending. Again, Keyes refused and gave Doubleday back their advance.[12] Five different publishers rejected the story over the course of a year[12] until it was published by Harcourt in 1966.

The short story "Flowers for Algernon" was first published as the lead story in the April 1959 issue of The Magazine of Fantasy and Science Fiction.[10] It was later reprinted in The Best from Fantasy and Science Fiction, 9th series (1960),[4][14] the Fifth Annual of the Year’s Best Science Fiction (1960),[4][15]Best Articles and Stories (1961),[4]Literary Cavalcade (1961),[4]The Science Fiction Hall of Fame, Volume One, 1929–1964 (1970),[16] and The Magazine of Fantasy & Science Fiction: A 30-Year Retrospective (1980).[14]

The expanded novel was first published in 1966 by Harcourt Brace with the Bantam paperback following in 1968.[4] By 2004, it had been translated into 27 languages, published in 30 countries and sold more than 5 million copies.[17] Since its original publication, the novel has never been out of print.[12]

The short story and the novel share many similar plot points, but the novel expands significantly on Charlie's developing emotional state as well as his intelligence, his memories of childhood, and the relationship with his family and Miss Kinnian.

The story is told through a series of journal entries written by the story's protagonist, Charlie Gordon, a man with a low IQ of 68 who works a menial job as a janitor in a factory. He is selected to undergo an experimental surgical technique to increase his intelligence. The technique had already been successfully tested on Algernon, a laboratory mouse. The surgery on Charlie is also a success, and his IQ triples.

Charlie falls in love with his former teacher, Miss Kinnian, but as his intelligence increases, he surpasses her intellectually, and they become unable to relate to each other. He also realizes that his co-workers at the factory, whom he thought were his friends, only liked him to be around so that they could make fun of him. His new intelligence scares his co-workers, and they start a petition to have him fired, but when Charlie finds out about the petition, he quits. As Charlie's intelligence peaks, Algernon's suddenly declines—he loses his increased intelligence and mental age, and dies shortly afterward, to be buried in a cheese box in the backyard of the lab where Charlie was tested. Charlie discovers that his intelligence increase is also only temporary. He starts to experiment to find out the cause of the flaw in the experiment, which he calls the "Algernon-Gordon Effect". Just when he finishes his experiments, his intelligence begins to regress to its state prior to the operation. Charlie is aware of, and pained by what is happening to him as he loses his knowledge and his ability to read and write. He tries to get his old job as a janitor back, and tries to revert to normal, but he cannot stand the pity from his co-workers, landlady, and Ms. Kinnian. Charlie states he plans to "go away" from New York and move to a new place. His last wish is that someone put flowers on Algernon's grave.

The novel opens with an epigraph discouraging people from laughing at those who are perplexed or weak of vision. The epigraph is taken from Plato'sThe Republic, part of which reads:

Any one who has common sense will remember that the bewilderments of the eye are of two kinds, and arise from two causes, either from coming out of the light or from going into the light, which is true of the mind's eye, quite as much as of the bodily eye.

—Plato, The Republic

Charlie Gordon, 32 years of age, suffers from phenylketonuria and has an IQ of 68. He holds a menial job at a bakery which his uncle had secured for him so that Charlie would not have to be sent to a state institution. Wanting to improve himself, Charlie attends reading and writing classes at the Beekman College Center for Retarded Adults; his teacher is Alice Kinnian, a young, attractive woman. Two researchers at Beekman are looking for a human test subject on whom to try a new surgical technique intended to increase intelligence. They have already performed the surgery on a mouse named Algernon, dramatically improving his mental performance. Based on Alice's recommendation and his own peerless motivation to improve, Charlie is chosen over smarter pupils to undergo the procedure.

The operation is a success, and within the next three months Charlie's IQ reaches an astonishing 185. However, as his intelligence, education, and understanding of the world around him increase, his relationships with people deteriorate. His co-workers at the bakery, who used to amuse themselves at his expense, are now scared and resentful of his increased intelligence and persuade his boss to fire him. One night at a cocktail party, a drunken Charlie angrily confronts his scientific mentors about their condescending attitude toward him. Charlie also embarks on a troubled romance with Alice. Unable to become intimate with the object of his affection, Charlie later starts a purely sexual relationship with Fay Lillman, a vivacious and promiscuous artist in the neighboring apartment.

When not drinking at night, Charlie spends intense weeks continuing his mentors' research on his own and writing reports which include observations of Algernon, whom he keeps at his apartment. Charlie's research discovers a flaw in the theory behind Nemur's and Strauss's intelligence-enhancing procedure, one that could eventually cause him to revert to his original mental state. His conclusions prove true when Algernon starts behaving erratically, loses his own enhanced intelligence, and dies.

Charlie tries to mend the long-broken relationships with his parents but without success. He remembered that as a boy his mother had insisted on his institutionalization, overruling his father's wish to keep him in the household. Charlie returns after many years to his family's Brooklyn home, and finds his mother now suffers from dementia and, although she recognizes him, is mentally confused. Charlie's father, who had broken off contact with the family many years before, does not recognize him when visited at his worksite. Charlie is only able to reconnect with his now-friendly younger sister, who had hated him for his mental disability when they were growing up, and who is now caring for their mother in their now-depressed neighborhood. Charlie promises to send her money.

As Charlie regresses intellectually, Fay becomes scared by the change and stops talking to him. However, Charlie finally attains sufficient emotional maturity to have a brief but fulfilling relationship with Alice, who cohabits with him until the extent of his mental deterioration causes him to finally order her to leave. Despite regressing to his former self, he still remembers that he was once a genius. He cannot bear to have his friends and co-workers feel sorry for him. Consequently, he decides to go away to live at the State-sponsored Warren Home School, where nobody knows about the operation. In a final postscript to his writings, ostensibly addressed to Alice Kinnian, he requests that she put some flowers on Algernon's grave in Charlie's former backyard.

Both the novel and the short story are written in an epistolary style, collecting together Charlie's personal "progress reports" from a few days before the operation until his final regression. Initially, the reports are full of spelling errors and awkwardly constructed sentences.[18] Following the operation, however, the first signs of Charlie's increased intelligence are his improved accuracy in spelling, grammar, and punctuation, and his word choice.[19][20] Charlie's regression is conveyed by the loss of these skills.[19]

Important themes in Flowers for Algernon include the treatment of the mentally disabled,[4][21][5] the impact on happiness of the conflict between intellect and emotion,[20][22][23] and how events in the past can influence a person later in life.[22]

In the late 1960s, the Science Fiction Writers of America (SFWA) decided to give Nebula Awards retroactively and voted for their favourite science fiction stories of the era ending 31 December 1964 (before the Nebula Award was conceived). The short story version of Flowers for Algernon was voted third out of 132 nominees and was published in The Science Fiction Hall of Fame, Volume One, 1929–1964 in 1970.[25] Keyes was elected the SFWA Author Emeritus in 2000 for making a significant contribution to science fiction and fantasy, primarily as a result of Flowers for Algernon.[26]

Flowers for Algernon is on the American Library Association's list of the 100 Most Frequently Challenged Books of 1990–1999 at number 43.[6] The reasons for the challenges vary, but usually center on those parts of the novel in which Charlie struggles to understand and express his sexual desires.[7] Many of the challenges have proved unsuccessful, but the book has occasionally been removed from school libraries, including some in Pennsylvania and Texas.[7][27]

In January 1970, the school board of Cranbrook, British Columbia, as well as Calgary, Alberta, removed the Flowers for Algernon novel from the local age 14-15 curriculum and the school library, after a parent complained that it was "filthy and immoral". The president of the British Columbia Teachers' Federation criticized the action. Flowers for Algernon was part of the British Columbia Department of Education list of approved books for grade nine and was recommended by the British Columbia Secondary Association of Teachers of English. A month later, the board reconsidered and returned the book to the library; they did not, however, lift its ban from the curriculum.[28][29]